I think one way to see the difference would be...
lit. As for John / Speaking of John, he is usually in Tokyo on holidays. (and someone else among the people we're talking about may also be in Tokyo.)
(Of all the people we are talking about) It is John (not someone else) who is usually in Tokyo on holidays. / John is the one who is usually in Tokyo on holidays.
The は is the topical/thematic は. Sentence 1 is usually said when ジョンさん is the topic of the conversation, i.e. ジョンさん has already been mentioned before this sentence is uttered, or the interlocuter(s) is/are expecting ジョンさん to be probably mentioned.
The が is the exhaustive が. Unlike wa, the subject particle ga nominates its referent as the sole satisfier of the predicate (quoted from here). So you'd usually say like ジョンさんが(東京に)いる (It is John who is in Tokyo) as a reply to a question 誰が東京にいますか？
If this line is from a story/novel, then the present form 触れる is the historical present (史的現在). Both sentences are grammatically correct, and one would be preferred over the other depending on the context.
You'd tend to use 彼は when 彼 has just done some other things or has just been mentioned, whereas you'd tend to use 彼が when you want to specifically say that it's 彼, not someone else, who does that action. (Thanks to @Sjiveru)
が also tends to be used in relative clauses and subordinate clauses, e.g. 「彼が傷口にそっと触れると、彼女は～～」「彼が傷口に触れた瞬間」
The は can also be the contrastive は. You can use the は to contrast 彼 (or 彼's action) with someone else (or their action). E.g. 「彼女は治療を拒んだが、彼は(not 彼が)傷口にそっと触れて…」